The GOA database: gene Ontology annotation updates for 2015

The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480 000 taxonomic groups. The resource now provides annotations to five times the number of proteins it did 4 years ago. As a member of the GO Consortium, we adhere to the most up-to-date Consortium-agreed annotation guidelines via the use of quality control checks that ensures that the GOA resource supplies high-quality functional information to proteins from a wide range of species. Annotations from GOA are freely available and are accessible through a powerful web browser as well as a variety of annotation file formats.

Integration of advanced oxidation processes at mild conditions in wet scrubbers for odourous sulphur compounds treatment

The effectiveness of different advanced oxidation processes on the treatment of a multicomponent aqueous solution containing ethyl mercaptan, dimethyl sulphide and dimethyl disulphide (0.5 mg L(-1) of each sulphur compound) was investigated with the objective to assess which one is the most suitable treatment to be coupled in wet scrubbers used in odour treatment facilities. UV/H2O2, Fenton, photo-Fenton and ozone treatments were tested at mild conditions and the oxidation efficiency obtained was compared. The oxidation tests were carried out in magnetically stirred cylindrical quartz reactors using the same molar concentration of oxidants (hydrogen peroxide or ozone). The results show that ozone and photo-Fenton are the most efficient treatments, achieving up to 95% of sulphur compounds oxidation and a mineralisation degree around 70% in 10 min. Furthermore, the total costs of the treatments taking into account the capital and operational costs were also estimated for a comparative purpose. The economic analysis revealed that the Fenton treatment is the most economical option to be integrated in a wet scrubber to remove volatile organic sulphur compounds, as long as there are no space constraints to install the required reactor volume. In the case of reactor volume limitation or retrofitting complexities, the ozone and photo-Fenton treatments should be considered as viable alternatives.

Contemporary wars and their contributions to vascular injury management

INTRODUCTION

Man's inhumanity for man still knows no boundaries, as we continue as a species as a whole to engage in war. According to Kohn's Dictionary of Wars [1], of over 3,700 years of recorded history, there have been a total of 3,010 wars. One is hard pressed to actually find a period of time in which here has not been an active conflict in the globe. The world has experienced two world wars: WWI (1914-1918) and WWII (1939-1945). The total number of military casualties in WWI was over 37 million, while WWII so far, has been the deadliest military conflict in history with over 60 million people killed accounting for slightly over 2.5% of the world's population.

MATERIAL AND METHODS

The purpose of this study is to review contemporary wars and their contributions to vascular injury management. It is precisely wartime contributions that have led to the more precise identification and management of these injuries resulting in countless lives and extremities saved. However, surgeons dealing with vascular injuries have faced a tough and arduous road. Their journey was initiated by surgical mavericks which undaunted, pressed on against all odds guided by William Stewart Halsted's classic statement in 1912: "One of the chief fascinations in surgery is the management of wounded vessels."

CONCLUSION

Contemporary wars of the XX-XXI centuries gave birth, defined and advanced the field of vascular injury management.

Atom-light interactions in photonic crystals

The integration of nanophotonics and atomic physics has been a long-sought goal that would open new frontiers for optical physics, including novel quantum transport and many-body phenomena with photon-mediated atomic interactions. Reaching this goal requires surmounting diverse challenges in nanofabrication and atomic manipulation. Here we report the development of a novel integrated optical circuit with a photonic crystal capable of both localizing and interfacing atoms with guided photons. Optical bands of a photonic crystal waveguide are aligned with selected atomic transitions. From reflection spectra measured with average atom number N=1.1+/-0.4, we infer that atoms are localized within the waveguide by optical dipole forces. The fraction of single-atom radiative decay into the waveguide is Γ1D/Γ'≃(0.32±0.08), where Γ1D is the rate of emission into the guided mode and Γ' is the decay rate into all other channels. Γ1D/Γ' is unprecedented in all current atom-photon interfaces.

Reduction of residual amplitude modulation to 1 × 10⁻⁶ for frequency modulation and laser stabilization

Active control and cancellation of residual amplitude modulation (RAM) in phase modulation of an optical carrier is one of the key technologies for achieving the ultimate stability of a laser locked to an ultrastable optical cavity. Furthermore, such techniques are versatile tools in various frequency modulation-based spectroscopy applications. In this Letter we report a simple and robust approach to actively stabilize RAM in an optical phase modulation process. We employ a waveguide-based electro-optic modulator (EOM) to provide phase modulation and implement an active servo with both DC electric field and temperature feedback onto the EOM to cancel both the in-phase and quadrature components of the RAM. This technique allows RAM control on the parts-per-million level where RAM-induced frequency instability is comparable to or lower than the fundamental thermal noise limit of the best available optical cavities.

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt

The Gene Ontology Consortium (GOC) is a major bioinformatics project that provides structured controlled vocabularies to classify gene product function and location. GOC members create annotations to gene products using the Gene Ontology (GO) vocabularies, thus providing an extensive, publicly available resource. The GO and its annotations to gene products are now an integral part of functional analysis, and statistical tests using GO data are becoming routine for researchers to include when publishing functional information. While many helpful articles about the GOC are available, there are certain updates to the ontology and annotation sets that sometimes go unobserved. Here we describe some of the ways in which GO can change that should be carefully considered by all users of GO as they may have a significant impact on the resulting gene product annotations, and therefore the functional description of the gene product, or the interpretation of analyses performed on GO datasets. GO annotations for gene products change for many reasons, and while these changes generally improve the accuracy of the representation of the underlying biology, they do not necessarily imply that previous annotations were incorrect. We additionally describe the quality assurance mechanisms we employ to improve the accuracy of annotations, which necessarily changes the composition of the annotation sets we provide. We use the Universal Protein Resource (UniProt) for illustrative purposes of how the GO Consortium, as a whole, manages these changes.

2'-fucosyllactose: an abundant, genetically determined soluble glycan present in human milk

Lactose is the preeminent soluble glycan in milk and a significant source of energy for most newborn mammals. Elongation of lactose with additional monosaccharides gives rise to a varied repertoire of free soluble glycans such as 2'-fucosyllactose (2'-FL), which is the most abundant oligosaccharide in human milk. In infants, 2'-FL is resistant to digestion and reaches the colon where it is partially fermented, behaving as soluble prebiotic fiber. Evidence also suggests that portions of small soluble milk glycans, including 2'-FL, are absorbed, thus raising the possibility of systemic biological effects. 2'-FL bears an epitope of the Secretor histo-blood group system; approximately 70-80% of all milk samples contain 2'-FL, since its synthesis depends on a fucosyltransferase that is not uniformly expressed. The fact that some infants are not exposed to 2'-FL has helped researchers to retrospectively probe for biological activities of this glycan. This review summarizes the attributes of 2'-FL in terms of its occurrence in mammalian phylogeny, its postulated biological activities, and its variability in human milk.

Optical spectrum analyzer with quantum-limited noise floor

Interactions between atoms and lasers provide the potential for unprecedented control of quantum states. Fulfilling this potential requires detailed knowledge of frequency noise in optical oscillators with state-of-the-art stability. We demonstrate a technique that precisely measures the noise spectrum of an ultrastable laser using optical lattice-trapped 87Sr atoms as a quantum projection noise-limited reference. We determine the laser noise spectrum from near dc to 100 Hz via the measured fluctuations in atomic excitation, guided by a simple and robust theory model. The noise spectrum yields a 26(4) mHz linewidth at a central frequency of 429 THz, corresponding to an optical quality factor of 1.6×10(16). This approach improves upon optical heterodyne beats between two similar laser systems by providing information unique to a single laser and complements the traditionally used Allan deviation which evaluates laser performance at relatively long time scales. We use this technique to verify the reduction of resonant noise in our ultrastable laser via feedback from an optical heterodyne beat. Finally, we show that knowledge of our laser's spectrum allows us to accurately predict the laser-limited stability for optical atomic clocks.

Comparison of two independent Sr optical clocks with 1×10(-17) stability at 10(3) s

Many-particle optical lattice clocks have the potential for unprecedented measurement precision and stability due to their low quantum projection noise. However, this potential has so far never been realized because clock stability has been limited by frequency noise of optical local oscillators. By synchronously probing two ^{87}Sr lattice systems using a laser with a thermal noise floor of 1×10(-15), we remove classically correlated laser noise from the intercomparison, but this does not demonstrate independent clock performance. With an improved optical oscillator that has a 1×10(-16) thermal noise floor, we demonstrate an order of magnitude improvement over the best reported stability of any independent clock, achieving a fractional instability of 1×10(-17) in 1000 s of averaging time for synchronous or asynchronous comparisons. This result is within a factor of 2 of the combined quantum projection noise limit for a 160 ms probe time with ~10(3) atoms in each clock. We further demonstrate that even at this high precision, the overall systematic uncertainty of our clock is not limited by atomic interactions. For the second Sr clock, which has a cavity-enhanced lattice, the atomic-density-dependent frequency shift is evaluated to be -3.11×10(-17) with an uncertainty of 8.2×10(-19).

Full phase stabilization of a Yb:fiber femtosecond frequency comb via high-bandwidth transducers

We present full phase stabilization of an amplified Yb:fiber femtosecond frequency comb using an intracavity electro-optic modulator and an acousto-optic modulator. These transducers provide high servo bandwidths of 580 kHz and 250 kHz for f(rep) and f(ceo), producing a robust and low phase noise fiber frequency comb. The comb was self-referenced with an f-2f interferometer and phase locked to an ultrastable optical reference used for the JILA Sr optical clock at 698 nm, exhibiting 0.21 rad and 0.47 rad of integrated phase errors (over 1 mHz-1 MHz), respectively. Alternatively, the comb was locked to two optical references at 698 nm and 1064 nm, obtaining 0.43 rad and 0.14 rad of integrated phase errors, respectively.

The impact of focused Gene Ontology curation of specific mammalian systems

The Gene Ontology (GO) resource provides dynamic controlled vocabularies to provide an information-rich resource to aid in the consistent description of the functional attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). System-focused projects, such as the Renal and Cardiovascular GO Annotation Initiatives, aim to provide detailed GO data for proteins implicated in specific organ development and function. Such projects support the rapid evaluation of new experimental data and aid in the generation of novel biological insights to help alleviate human disease. This paper describes the improvement of GO data for renal and cardiovascular research communities and demonstrates that the cardiovascular-focused GO annotations, created over the past three years, have led to an evident improvement of microarray interpretation. The reanalysis of cardiovascular microarray datasets confirms the need to continue to improve the annotation of the human proteome.

AVAILABILITY

GO ANNOTATION DATA IS FREELY AVAILABLE FROM: ftp://ftp.geneontology.org/pub/go/gene-associations/

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set.

A tripartite complex composed of ETV6-NTRK3, IRS1 and IGF1R is required for ETV6-NTRK3-mediated membrane localization and transformation

ETV6-NTRK3 (EN), a chimeric tyrosine kinase generated by t(12;15) translocations, is a dominantly acting oncoprotein in diverse tumor types. We previously showed that insulin-like growth factor 1 receptor (IGF1R) is essential for EN-mediated oncogenesis and that insulin receptor substrate 1 (IRS1) is constitutively tyrosine phosphorylated and bound by EN in transformed cells. Given that IRS1 is also an adapter for IGF1R, we hypothesized that IRS1 might localize EN to IGF1R at the membrane to activate phosphatidylinositol 3-kinase (PI3K)-Akt, which is critical for EN oncogenesis. In this study, we examined EN/IRS1/IGF1R complexes in detail. We find that both IRS1 and kinase active IGF1R are required for EN transformation, that tyrosine phosphorylated IRS1 is present in high molecular weight complexes with EN and IGF1R, and that EN colocalizes with IGF1R at the plasma membrane. Both IGF1R kinase activity and an intact cytoplasmic Y950 residue, the IRS1-docking site of IGF1R, are required, confirming the importance of the IGF1R/IRS1 interaction for EN oncogenesis. The dual specificity IGF1R and insulin receptor (INSR) inhibitor, BMS-536924, blocks EN transformation activity, cell survival and its interaction with IRS proteins, and induces a striking shift of EN proteins to smaller sized molecular complexes. We conclude that a tripartite complex of EN, IRS1 and IGF1R localizes EN to the membrane and that this is essential for EN-mediated transformation. These findings provide an explanation for the observed IGF1R dependency of EN transformation. Blocking IGF1R kinase activity may, therefore, provide a tractable therapeutic strategy for the many tumor types driven by the EN oncoprotein.

Gastric anti-ulcer activity of silymarin, a lipoxygenase inhibitor, in rats

Oral treatment with silymarin was found to be effective in the prevention of gastric ulceration induced by cold-restraint stress, in rats. Statistically significant ulcer index values with respect to the control group, were observed. In 6 h pyloric-ligated animals silymarin showed a significant reduction in the number and severity of the ulcers; however, it did not alter the gastric secretion volume or acidity although histamine concentration was significantly decreased. In absolute ethanol-induced ulcers, treatment with silymarin 1 or 2 h before the anti-ulcerogenic agent, did not prevent the formation of gastric lesions. Furthermore, the hexosamine content was decreased significantly, but the total protein output was enhanced, showing similar values to those with the standard drug, carbenoxolone. These results suggest that the anti-ulcerogenic effect of silymarin could be related to its inhibitory mechanism of enzymatic peroxidation by the lipoxygenase pathway, avoiding leukotriene synthesis.

Structure of a preternary complex involving a prokaryotic NHEJ DNA polymerase

In many prokaryotes, a specific DNA primase/polymerase (PolDom) is required for nonhomologous end joining (NHEJ) repair of DNA double-strand breaks (DSBs). Here, we report the crystal structure of a catalytically active conformation of Mycobacterium tuberculosis PolDom, consisting of a polymerase bound to a DNA end with a 3' overhang, two metal ions, and an incoming nucleotide but, significantly, lacking a primer strand. This structure represents a polymerase:DNA complex in a preternary intermediate state. This polymerase complex occurs in solution, stabilizing the enzyme on DNA ends and promoting nucleotide extension of short incoming termini. We also demonstrate that the invariant Arg(220), contained in a conserved loop (loop 2), plays an essential role in catalysis by regulating binding of a second metal ion in the active site. We propose that this NHEJ intermediate facilitates extension reactions involving critically short or noncomplementary DNA ends, thus promoting break repair and minimizing sequence loss during DSB repair.

Abstract P5-10-17: Bevacizumab (Bev) in Combination with Docetaxel (T) and Cyclophosphamide (C) as Adjuvant Treatment (AdjRx) for Patients (pts) with Early Stage (ES) Breast Cancer (BrCa) and Normal HER-2 Status. A Pilot Evaluation

In random assignment trials, the combination of Bev+ chemotherapy has been shown to produce superior response rates and progression free survival compared to chemotherapy alone, providing a rationale for the study of Bev in the AdjRx of pts with ESBrCa. As a principal side effect of Bev is hypertension (HTN), anthracycline-containing (Anth) AdjRx may pose additional cardiovascular risks. The role of Anth in Her2 normal ESBC is uncertain. TC is a standard non-Anth AdjRx. We performed a single arm pilot study to evaluate the feasibility and toxicity of TC+Bev in pts with ESBC in preparation for participation in a random assignment trial. Methods: Eligibility criteria included: ESBC which was HER-2 normal, node-positive or >2 cm and receptor negative, or >3 cm and receptor positive, normal cardiac ejection fraction (EF), no active or uncontrolled cardiovascular disease, normal organ and marrow function. Treatment consisted of four 3 weekly cycles of docetaxel 75 mg/m2 together with cyclophosphamide 600 mg/m2. Patients commenced bevacizumab 15 mg/kg i.v. on day 1, and q 3 weeks to a total of 19 treatments. Pts were monitored clinically, with echocardiograms and with serial estimations of BNP and troponin.

Results: A total of 105 female pts were accrued in 9 ICORG sites between Dec 2008 and June 2010. Ages ranged from 26-86 (median 55). At June 2010, 33 have completed all phases of therapy, 54 are still on treatment. Eighteen pts have been removed from study due to: HTN -7, intestinal perforation -2, withdrew consent-4, proteinuia-1, anaphylaxis-1, infection-3. The perforations occurred at cycles 9 and 19. Neither pt. with perforation had prior abdominal surgery. The median number of cycles achieved by the discontinued pts was 9. HTN requiring Rx occurred in 25 pts. Among 12 with HTN who have completed Bev, 2 are off HTN meds, and 9 are on reducing doses. The median EF at base line was 67%, at 13 cycles (42 pts) 63%, 18 cycles (27 pts) 66%. Six pts had EF drop >10%, in 3 of these EF fell below 50% as last recorded value. There were no episodes of clinical cardiac failure. Troponin and BNP levels were normal in all 57 pts with serial measurements. Thirteen pts required treatment for neutropenia-related infection or for abscess.

Conclusions: The spectrum and frequency of bevacizumab toxicity in our population of healthy adjuvant pts is similar to that reported for pts with metastatic BC and other malignancies. Hypertension is the principal cause of treatment discontinuation, but cardiac toxicity appears to be limited, with this non-anth chemotherapy +Bev. Intestinal perforation can also occur in pts with ESBC. These toxicities can occur in the post chemotherapy phase of Bev therapy. Pts enrolled on random assignment trials of Bev containing AdjRx require careful monitoring for toxicity.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P5-10-17.

Infrastructure for the life sciences: design and implementation of the UniProt website

BACKGROUND

The UniProt consortium was formed in 2002 by groups from the Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) at Georgetown University, and soon afterwards the website http://www.uniprot.org was set up as a central entry point to UniProt resources. Requests to this address were redirected to one of the three organisations' websites. While these sites shared a set of static pages with general information about UniProt, their pages for searching and viewing data were different. To provide users with a consistent view and to cut the cost of maintaining three separate sites, the consortium decided to develop a common website for UniProt. Following several years of intense development and a year of public beta testing, the http://www.uniprot.org domain was switched to the newly developed site described in this paper in July 2008.

DESCRIPTION

The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. These tools include full text and field-based text search, similarity search, multiple sequence alignment, batch retrieval and database identifier mapping. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.http://www.uniprot.org/ is open for both academic and commercial use. The site was built with open source tools and libraries. Feedback is very welcome and should be sent to help@uniprot.org.

CONCLUSION

The new UniProt website makes accessing and understanding UniProt easier than ever. The two main lessons learned are that getting the basics right for such a data provider website has huge benefits, but is not trivial and easy to underestimate, and that there is no substitute for using empirical data throughout the development process to decide on what is and what is not working for your users.

Apnoeic and obstructive nonapnoeic sleep respiratory events

Obstructive nonapnoeic event (ONE) scoring is shrouded in confusion. This is important in patients with mild disease, in whom precision is crucial. The aims of the present study were: 1) to identify ONEs using oesophageal pressure (OP) (OP-ONEs) and a noninvasive (NI) method (NI-ONEs); 2) to compare both methods of scoring; and 3) to determine the contribution of ONE definitions to clinical findings. Patients with suspected sleep apnoeas (respiratory disturbance index <or=10) during a first polysomnography were subjected to a second with an OP measurement. OP-ONEs and NI-ONEs were defined as an increase in OP or discernible reduction in the amplitude of thoracoabdominal bands with both desaturation and/or arousal. Bland-Altman analysis established agreement. Comparisons were made between OP-ONEs, NI-ONEs and clinical findings. In our sample (n = 90), the addition of an arousal to the NI-ONEs or OP-ONEs with only desaturation increased the number of NI-ONEs by 329 and 362%, respectively. NI-ONEs with arousal and/or desaturation detected 91% of OP-ONEs. The association with sleepiness depended on the incorporation of arousal into the definition of ONEs. In patients with mild disease, the addition of an arousal to ONEs, with only desaturation, markedly increased respiratory disturbance index, with probable therapeutic implications. Scoring respiratory events as apnoea and ONEs is easier and sufficiently accurate.

Removal of odour-causing compounds using carbonaceous adsorbents/catalysts prepared from sewage sludge

This paper discusses H(2)S, NH(3) and VOCs removal by sewage-sludge-derived materials with outstanding chemical and textural properties. These materials were obtained from different precursors using different chemical and thermal treatments. Results show that the H(2)S removal process entailed a catalytic conversion of H(2)S to S or SO(4) (2-) species. On the other hand, adsorption is the main mechanism governing the performance of sludge-based materials for NH(3) and VOCs. Retention capacities (x/M values) obtained for some of the sludge-based adsorbents/catalysts are similar to those obtained with commercial activated carbons selected as reference materials.

Sr lattice clock at 1 x 10(-16) fractional uncertainty by remote optical evaluation with a Ca clock

Optical atomic clocks promise timekeeping at the highest precision and accuracy, owing to their high operating frequencies. Rigorous evaluations of these clocks require direct comparisons between them. We have realized a high-performance remote comparison of optical clocks over kilometer-scale urban distances, a key step for development, dissemination, and application of these optical standards. Through this remote comparison and a proper design of lattice-confined neutral atoms for clock operation, we evaluate the uncertainty of a strontium (Sr) optical lattice clock at the 1 x 10(-16) fractional level, surpassing the current best evaluations of cesium (Cs) primary standards. We also report on the observation of density-dependent effects in the spin-polarized fermionic sample and discuss the current limiting effect of blackbody radiation-induced frequency shifts.

The Universal Protein Resource (UniProt): an expanding universe of protein information

The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics. The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/TrEMBL section, is the preeminent storehouse of protein annotation. The extensive cross-references, functional and feature annotations and literature-based evidence attribution enable scientists to analyse proteins and query across databases. The UniProt Reference Clusters (UniRef) speed similarity searches via sequence space compression by merging sequences that are 100% (UniRef100), 90% (UniRef90) or 50% (UniRef50) identical. Finally, the UniProt Archive (UniParc) stores all publicly available protein sequences, containing the history of sequence data with links to the source databases. UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described. New download availability includes all major releases of UniProtKB, sequence collections by taxonomic division and complete proteomes. A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at or downloaded at .

Dried sludges and sludge-based chars for H2S removal at low temperature: influence of sewage sludge characteristics

The use of sewage sludge as a precursor of adsorbent/ catalyst materials for environmental applications has been encouraged during the past few years. Due to the heterogeneous nature of sludges, there exists a lack of information regarding the characteristics of these low-cost precursors and how their physicochemical properties affect the final performance of materials prepared from them. In this work, three sewage-sludges collected at WWTPs with assorted sludge/wastewater treatment schemes were used as precursors of adsorbents/catalysts for H2S removal at room temperature. All the solidswere characterized to establish their textural properties and chemical composition, including the speciation of the adsorbents/ catalysts inorganic fraction. Thermal treatment (gasification) of the raw (dried) sludges increased the H2S removal ability in all cases. For these thermally treated materials, catalytic conversion to elemental sulfur and sulfate moieties was found to be the main route of H2S removal. Results indicate that adsorbents based on an iron/calcium-containing sludge were the most reactive and exhibited the highest capacities for H2S retention. Forthis particulartype of sludge, a reasonably good performance was observed even when the dried (raw) sludge was used as adsorbent/ catalyst. Alternatively, the oxidation of H2S by chars obtained from the other two sludges under study was related to their textural properties.

A novel mathematical model identifies potential factors regulating bone apposition

The development of pharmaceutical treatments for bone disease can be enhanced by mathematical models that predict their effects on matrix apposition during cancellous bone remodelling. Therefore, a mathematical model was constructed to simulate the rate of focal bone formation from the number of osteoid-forming osteoblasts at one microsite and their rate of activity. The number of mature osteoid-forming cells was simulated from a relationship describing the proliferation of preosteoblasts. Osteoblast activity was described by Michaelis-Menten enzyme kinetic equations adapted to describe cellular activity. The model incorporates the negative feedback effects on the rates of bone apposition due to the reduction in size of mature osteoblasts with continuing differentiation and the reduction in number of osteoid-forming cells with apoptosis and osteocyte formation. In addition, the rate of mineralisation is limited according to osteoid substrate availability. Results of sensitivity analysis revealed the amount of bone formed at one microsite to be more sensitive to changes in factors that controlled cell growth during proliferation and the number of mature osteoid-forming osteoblasts than to those that determined cellular activity. Matrix and osteocyte signalling were shown to have potentially important roles in controlling rates of osteoid apposition in normal, healthy bone. This simple model supports the critical role of controlled mitotic growth in normal bone apposition. It can also help to explain how the homeostatic processes of bone resorption and apposition during remodelling can be disrupted by growth factors that affect the mitotic fraction and division time of proliferative preosteoblast cells.